/*
 * Copyright 2006-2018 The MZmine 2 Development Team
 * 
 * This file is part of MZmine 2.
 * 
 * MZmine 2 is free software; you can redistribute it and/or modify it under the terms of the GNU
 * General Public License as published by the Free Software Foundation; either version 2 of the
 * License, or (at your option) any later version.
 * 
 * MZmine 2 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
 * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 * General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License along with MZmine 2; if not,
 * write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301
 * USA
 */

package net.sf.mzmine.modules.peaklistmethods.isotopes.isotopepatternscore;

import net.sf.mzmine.main.MZmineCore;
import net.sf.mzmine.parameters.Parameter;
import net.sf.mzmine.parameters.impl.SimpleParameterSet;
import net.sf.mzmine.parameters.parametertypes.DoubleParameter;
import net.sf.mzmine.parameters.parametertypes.PercentParameter;
import net.sf.mzmine.parameters.parametertypes.tolerances.MZToleranceParameter;

public class IsotopePatternScoreParameters extends SimpleParameterSet {

  public static final MZToleranceParameter mzTolerance =
      new MZToleranceParameter("Isotope m/z tolerance",
          "m/z tolerance which defines what isotopes would be considered same when "
              + "comparing two isotopic patterns. This tolerance needs to be "
              + "higher than general m/z precision of the data, because some "
              + "small isotopes may overlap with the sides of bigger isotopic " + "peaks.");

  public static final DoubleParameter isotopeNoiseLevel = new DoubleParameter(
      "Minimum absolute intensity",
      "Minimum absolute intensity of the isotopes to be compared. Isotopes below this intensity will be ignored.",
      MZmineCore.getConfiguration().getIntensityFormat());

  public static final PercentParameter isotopePatternScoreThreshold = new PercentParameter(
      "Minimum score", "If the score between isotope pattern is lower, discard this match");

  public IsotopePatternScoreParameters() {
    super(new Parameter[] {mzTolerance, isotopeNoiseLevel, isotopePatternScoreThreshold});
  }

}
